MolNFT v1 · #17932 · protein + DNA
The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor
1P8K · 5'- D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C…: “The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor”. X-ray diffraction, 1 ligand (MG), 2 pockets (best…
- PDB
- 1P8K
- Type
- protein + DNA
- Length
- 316 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)- 3'…
- EC
- 3.1.-.-
- UniProt
- P03880
- Ligands
- MG
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'- D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)- 3' | dna | 18 | — | — |
| B | 5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3' | dna | 13 | — | — |
| C | 5'- D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3' | dna | 16 | — | — |
| D | 5'- D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3' | dna | 15 | — | — |
| Z | Intron-encoded endonuclease I-anii (EC 3.1.-.-) | protein | 254 | 45% helix, 20% strand | P03880 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, D, Z, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.50 | 0.85 | 17 | empty |
| 2 | 120 | 0.42 | 0.77 | 18 | empty |
Interfaces
9 interfaces between chains.
- C–Z · 923 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–Z · 896 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–D · 702 Ų buried · 52 hydrogen bonds · nucleic-nucleic
- B–C · 628 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- B–Z · 587 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (engineered).
Compared structures
- 1P8K · The structure and DNA recognition of a bifunctional homing endonuclease and group I… · the same entry in another collection · chain A against A, TM-score 1.00
- P03880 · AlphaFold monomer V2.0 prediction for intron-encoded DNA endonuclease I-anii (P03880) · a predicted model of the same protein · chain Z against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P03880
- Elsewhere: RCSB PDB 1P8K · PDBe 1P8K · UniProt P03880
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